Contacts of the strand formed by residues 131 - 139 (chain D) in PDB entry 2ONL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B GLN* 5.7 4.9 - - - +
127D LEU* 3.9 6.6 - - - +
128D TYR* 3.0 31.5 + - - +
129D ALA* 2.8 25.5 + - + +
130D GLY* 1.3 88.9 + - - +
132D LYS* 1.3 67.9 + - - +
133D CYS* 3.3 10.7 + - - +
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Residues in contact with LYS 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLN* 4.6 2.3 - - - -
97D ASP* 3.7 50.4 + - + +
125D GLU* 4.1 17.4 - - - +
126D ASN 3.6 6.7 - - - -
127D LEU* 4.8 10.5 - - + +
131D ARG* 1.3 72.3 - - - +
133D CYS* 1.3 62.6 + - - +
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Residues in contact with CYS 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D MET* 4.6 24.9 - - - -
95D LEU 3.8 16.8 - - - -
96D GLN* 5.2 1.8 - - - -
97D ASP* 4.4 2.7 - - - +
125D GLU* 4.8 0.2 + - - -
126D ASN 2.7 25.8 + - - +
128D TYR* 5.1 9.6 - - + +
131D ARG* 3.3 14.1 + - - +
132D LYS* 1.3 77.2 - - - +
134D LEU* 1.3 59.1 + - - +
135D LEU* 2.8 41.0 + - + +
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 3.7 14.8 - - + -
93D LYS 4.2 0.2 - - - +
94D MET* 4.0 0.5 - - - -
95D LEU* 3.2 40.3 + - + +
97D ASP* 2.8 33.6 - - - +
101D ALA* 3.4 27.1 - - + +
102D ARG* 3.2 33.2 - - + +
105D VAL* 3.8 19.7 - - + -
123D VAL* 4.2 9.9 - - + -
124D TYR 3.3 10.8 - - - +
125D GLU* 4.2 3.1 - - - -
133D CYS* 1.3 69.0 - - - +
135D LEU* 1.3 59.7 + - - +
136D ILE* 3.6 7.6 + - + +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ILE* 5.9 7.0 - - + -
92D LEU* 3.9 21.3 - - + -
93D LYS 4.1 4.5 - - - -
94D MET* 4.2 28.0 - - + +
122D ASP 3.6 4.0 - - - +
124D TYR* 2.7 41.8 + - + +
126D ASN* 2.8 33.2 - - + -
128D TYR* 5.7 10.1 - - + -
133D CYS* 2.8 40.7 + - + +
134D LEU* 1.3 71.6 - - - +
136D ILE* 1.3 64.4 + - - +
137D VAL* 4.0 0.9 - - - +
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ALA 3.8 0.2 - - - +
92D LEU* 2.8 32.1 - - - +
93D LYS* 3.3 17.8 + - + +
95D LEU* 3.0 36.6 - - + -
104D GLU* 5.2 1.8 - - - +
105D VAL* 3.5 27.6 - - + -
108D HIS* 6.1 2.2 - - + +
120D ILE* 4.2 22.0 - - + -
122D ASP 3.8 2.5 - - - -
123D VAL* 4.2 25.1 - - + +
134D LEU* 4.3 7.0 - - + +
135D LEU* 1.3 73.5 - - - +
137D VAL* 1.3 60.6 + - - +
138D MET* 4.0 13.3 + - + +
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Residues in contact with VAL 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ILE* 3.5 27.6 - - + -
90D PHE* 3.9 15.3 - - + -
91D ALA 3.3 5.6 - - - +
92D LEU* 3.8 13.0 - - + -
120D ILE* 3.5 1.4 - - - +
121D VAL* 2.5 51.2 + - + +
122D ASP* 2.9 24.4 + - + +
124D TYR* 3.8 22.7 - - + -
136D ILE* 1.3 77.9 - - - +
138D MET* 1.3 55.6 + - - +
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Residues in contact with MET 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D VAL* 5.3 6.3 - - + -
90D PHE* 3.8 3.9 - - - -
91D ALA* 2.8 54.7 + - + +
93D LYS* 4.6 17.5 - - + -
108D HIS* 5.5 8.5 - - + -
118D VAL* 4.1 16.2 - - + -
119D ARG 3.3 13.5 - - - +
120D ILE* 3.9 8.1 - - + -
121D VAL* 4.0 4.0 - - - +
136D ILE* 4.3 17.5 - - + +
137D VAL* 1.3 76.5 - - - +
139D GLU* 1.3 89.2 + - - +
141D LEU* 4.9 4.7 - - + +
206D THR* 5.9 4.3 - - - +
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Residues in contact with GLU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D LYS 4.8 0.9 - - - -
90D PHE* 4.4 10.5 - - + -
118D VAL* 3.6 11.9 - - + +
119D ARG* 2.7 60.3 + - + +
121D VAL* 4.0 4.2 - - + +
138D MET* 1.3 94.0 - - - +
140D CYS* 1.3 71.5 + - - +
141D LEU* 3.8 4.4 + - + -
195D THR* 4.0 13.9 - - - +
204D LYS* 3.6 26.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il